Just need confirmation of whether I am constructing the correct design matrix

I am working with 2-color Agilent arrays. I've bg-corrected and normalized the expression values. The goal of the experiment is to see if there's differential expression between pre-treatment and post-treatment with a drug.

The microarrays were formatted as follows:

pre = pre- drug treatment
post = post- drug treatment 

                 file           Cy3       Cy5
Array 1      file1.txt          pre       pre
Array 2      file2.txt          pre       post
Array 3      file3.txt          pre       pre
Array 4      file4.txt          post      pre
Array 5      file5.txt          post      pre
Array 6      file6.txt          pre       post

Is design <- modelMatrix(targets, ref="pre") an accurate design matrix? or does the pre-pre arrays need separate analysis?

Any guidance would be appreciated.